Tilapia culture has expanded rapidly worldwide, especially in Southeast Asia, including Thailand, Vietnam, Indonesia, India, Taiwan and China. Large-scale commercial culture of tilapia almost exclusively involves three species: Oreochromis niloticus , Oreochromis mossambicus and Oreochromis aureus , of which the Nile tilapia, O niloticus , is the most commonly farmed species. Infectious diseases pose constant and serious threats to fish that are intensively farmed under conditions of high population density, poor water quality and poor farm management. Currently, however, tilapia culture is most at risk from emerging viral and bacterial infections and novel parasitic diseases (Shoemaker and others 2000, Adeyemo and Agbede 2008). Diplomonad flagellate are commonly found in a wide variety of hosts, from mammals to fish. They can infect a wide range of fish species both fresh and marine water, across a broad geographic range from coldwater fish farms to tropical areas (Kent and others 1992, Poynton and others 1995, Koudela and others 1996, Sterud and others 1998). Red tilapia cultured in earthen ponds in Songkhla Province demonstrated some clinical abnormalities. Tilapia fingerlings showed distinct clinical signs: emaciation and multiple white nodules in muscle tissue. Although the infected fish swam normally, the distinct white nodules made them the subject of attack by healthy fish, and they ultimately died from the resultant wounds. Consequently, one hundred and fifty red tilapia, average weight 5–10 g were collected from earthen ponds in Angthong Province, and transported live to the Aquatic Animal Health Research Center, Prince of Songkla University, Had Yai, Thailand. Sampled fish were examined macroscopically and then anesthetised with 50 ppm quinaldine (Muench 1958). Subsequently, fish were dissected and gill, liver, kidney, gall bladder and intestine tissues were sampled for the …